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Re: Trying to use imgCIF/CBF

• To: imgcif-l@bnl.gov
• Subject: Re: Trying to use imgCIF/CBF
• From: "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>
• Date: Tue, 23 Jan 2001 13:54:15 -0500
• In-Reply-To: <Pine.SGI.3.96.1010123120156.15095E-100000@lsx12n.nsls.bnl.gov>

A few comments:


>## Note: the specimen-to-detector distance is defined in the
>   frame scan-axis items as given below from the IUCr imgCIF definition
>   http://www.iucr.org/iucr-top/cif/imgcif/cif_img_1.0.html#DIFFRN_SCAN:
>
>   loop_
>      _diffrn_scan_axis.scan_id
>      _diffrn_scan_axis.axis_id
>      _diffrn_scan_axis.angle_start
>      _diffrn_scan_axis.angle_increment
>      _diffrn_scan_axis.displacement_start
>      _diffrn_scan_axis.displacement_range
>      _diffrn_scan_axis.displacement_increment
>
>       1 omega 200.0 20.0 0.1 . . .
>       1 kappa -40.0  0.0 0.0 . . .
>       1 phi   127.5  0.0 0.0 . . .
>       1 tranz  . . .   2.3 0.0 0.0
>
>In the simplest case this tranz value should define the
>specimen-to-detector distance.
>
>{I don't see why the tranz displacement is given as 2.3 in the
>example.  This should be mm, and should be on the order of 100.}

There are two aspects to displacement -- displacement _of_ the axis, and
displacement _along_ the axis.  See the data items in the AXIS category
for specification of the  displacement _of_ the axis:  _axis.offset[1],
_axis.offset[2], _axis.offset[3].  Certainly, in handling tranz, it would
be reasonable either to put the large value (100) into the axis definition,
or into the displacement along the axis, but I would suggest that for an
axis allowing for very fine steps, we would achieve better clarity (and
numeric precision) by putting the large value into the axis definition and
the small increments into the scan offsets.

The actual axis settings for a given exposure should be given using tags from
DIFFRN_SCAN_FRAME_AXIS.

  -- Herbert


At 12:18 -0500 1/23/01, Robert Sweet wrote:
>John Westbrook, Paul Ellis, and I have been having a conversation about
>where to go with this, and I'm writing this note to try to draw anyone
>else who wants to be back into the discussion.
>
>I've been trying to decide what a truly usable header should look like.  I
>have written some comments and questions, essentially in the form of
>searching for the right CIF entries, which I include below.  You'll see
>that I use a couple of entries that Harry Powell invented, and that my
>comments end with a serious question.  I'll look forward to having some
>advice.
>
>----------------------
 ...

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